Contacts of the strand formed by residues 164 - 170 (chain C) in PDB entry 4BEI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160C GLU* 3.3 3.0 - - - -
161C LEU* 2.8 56.3 + - + +
162C ASN 3.3 1.8 + - - -
163C GLY* 1.3 72.8 - - - +
165C THR* 1.3 58.3 + - - +
166C ILE* 3.4 12.8 - - + +
190C LEU* 4.4 8.3 - - + -
191C ASN 3.4 22.2 - - - +
192C ASN* 3.5 26.0 - - + +
193C GLY 4.3 1.6 - - - +
194C ARG* 4.1 12.8 - - - +
198C ALA* 4.3 8.5 - - + -
200C VAL* 3.3 36.3 - - + -
224C ILE* 4.4 10.3 - - + -
253C VAL* 4.7 2.2 - - + -
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Residues in contact with THR 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C LEU* 3.7 27.1 - - + +
159C PRO 3.8 6.1 - - - -
160C GLU* 4.0 13.5 - - + +
163C GLY* 3.6 14.8 - - - +
164C LEU* 1.3 74.6 - - - +
166C ILE* 1.3 63.2 + - - +
167C ASP* 5.1 1.0 + - - +
189C ASP 3.8 1.0 + - - +
190C LEU* 3.4 4.7 - - - +
191C ASN* 2.8 57.3 + - - +
193C GLY* 5.3 1.1 - - - +
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Residues in contact with ILE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LEU* 3.7 7.1 - - - +
159C PRO* 2.9 39.8 + - + +
161C LEU* 4.5 4.3 - - + +
164C LEU* 3.4 30.5 - - + +
165C THR* 1.3 76.4 - - - +
167C ASP* 1.3 61.6 + - - +
168C ILE* 3.4 28.9 - - + -
189C ASP 3.7 1.8 - - - -
190C LEU* 4.2 9.6 - - + -
251C ALA 6.1 0.2 - - - +
253C VAL* 3.6 31.6 - - + -
262C VAL* 3.9 23.1 - - + -
264C GLN* 3.6 13.9 - - + +
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Residues in contact with ASP 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C LEU* 3.6 33.4 - - + +
165C THR* 5.3 1.3 - - - +
166C ILE* 1.3 74.5 - - - +
168C ILE* 1.3 62.5 + - - +
169C LYS* 3.2 39.4 + - - +
187C THR* 3.5 5.7 + - - +
189C ASP* 2.7 54.6 + - + +
264C GLN* 4.2 1.6 - - - +
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Residues in contact with ILE 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ILE* 3.4 31.2 - - + -
167C ASP* 1.3 76.0 + - - +
169C LYS* 1.3 70.4 + - - +
186C PHE* 4.7 4.3 - - + -
187C THR 3.3 10.5 - - - +
188C VAL* 4.1 19.7 - - + -
190C LEU* 4.7 1.6 - - + -
202C PHE* 4.5 11.9 - - + -
204C MET* 4.3 15.9 - - + -
251C ALA* 3.5 26.7 - - + -
253C VAL* 5.3 1.1 - - + -
264C GLN* 3.4 29.6 + - + +
266C MET* 3.7 35.8 - - + +
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Residues in contact with LYS 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ASP* 3.2 35.4 + - - +
168C ILE* 1.3 81.3 - - - +
170C ASN* 1.3 63.9 + - - +
171C GLN* 3.0 5.3 + - - -
186C PHE* 3.3 9.6 - - - -
187C THR* 2.9 46.9 + - - +
189C ASP* 5.5 3.0 + - - -
266C MET* 4.2 2.5 - - - -
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Residues in contact with ASN 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C LYS* 1.3 70.9 - - - +
171C GLN* 1.3 65.8 + - - +
172C PHE 3.1 4.2 + - - -
173C GLY* 3.1 13.7 + - - -
174C ILE* 2.7 49.5 + - - +
175C ASN* 4.4 8.0 - - - +
184C VAL* 3.7 20.9 - - - +
185C PRO* 4.2 0.7 - - - +
186C PHE* 3.5 23.3 - - + -
266C MET* 4.0 13.8 - - + +
267C THR 5.2 1.2 + - - -
268C VAL* 4.2 6.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il